The extended x-ray-absorption fine structure EXAFS Debye-Waller factor is an essential term appearing in EXAFS theory, and that accounts for the structural and thermal disorder of a sample. Single-and multiple-scattering Debye-Waller factors must be known accurately to obtain quantitative agreement between theory and experiment. Since the total number of parameters that can be determined by fitting experimental data is limited, in general, data cannot support fitting of all relevant multiple-scattering Debye-Waller factors. We have developed the ability to calculate these ab initio multiple scattering DWFs directly from the known or hypothetical three-dimensional structure. This is a necessary first step toward a practical approach to multiple scattering fitting, without use of fudge-factors. In our first paper (published in Phys. Rev. B.) we investigated the adequacy of various computational approaches for calculating vibrational structure within small molecules. Analytical expressions were derived for multiple scattering Debye-Waller factors, based on the plane wave approximation, which appears to be adequate for this purpose. Both semiempirical Hamiltonians (ZINDO) and the ab initio density functional programs (DGAUSS) were used to calculate the normal mode eigenfrequencies and eigenvectors. Using programs written in-house, these data were used to calculate all single- and multiple-scattering Debye-Waller factors up to a four atom cluster. The ab initio Debye-Waller factors were compared to those calculated from experimental infrared and Raman frequencies. Good agreement was observed for all cases, lending strong support for the feasibility of calculating accurate multiple scattering debye waller factors for amino acid residues in proteins.